Integrative single-cell RNA-seq and ATACseqanalysis of B-cell and T-cell clusters revealed differentiallyaccessible chromatin regions in invasive breast cancer

Background: Breast cancer is the predominant form of malignancyin women, often resulting in metastasis and being aleading cause of cancer-related mortalities, with an estimatednew diagnosis of ۳۰۰,۵۹۰ and ۴۳,۷۰۰ deaths for both sexes in۲۰۲۳. Single-cell technologies enabled us to identify propertiesof tumor-infiltrating immune cells, including T-cell and B-cellsubpopulations in the tumor microenvironment. The comprehensivecancer study required the integrative profiling of geneticand epigenetic changes at single-cell resolution. Single-cellassay for transposase-accessible chromatin with sequencing(scATAC-seq) detects open chromatin in individual cells. Thisresearch aims to investigate the immune system's genomics andepigenomics aspects in cancer by studying B cell and T cellsubpopulations with an integrative single-cell ATAC-seq andRNA-seq analysis approach.Materials and Methods: HiSeq x۱۰ Single-cell transcriptomedata and ATAC-seq data produced by Illumina novaSeq۶۰۰۰of the positive lymph nodes in metastatic breast cancer weredownloaded from the gene expression omnibus database underaccession numbers GSE۱۵۸۳۹۹ and GSE۱۵۸۳۹۸, respectively.Seurat and Signac packages were utilized to perform qualitycontrol and analysis on each dataset separately. Filtrationswere performed based on transcription start site (TSS), nucleosomesignal, feature counts, and mitochondrial count percentages.Transcriptome and epigenome data were integrated usingcross-modality integration and transfer label method. Labelingof cellular clusters was done with the SingleR package andCellMarker۲. The results of the analysis were plotted using theggplot۲ package of R.Results: Low-quality cells of scATAC-seq and scRNA-seqwere filtered out then normalization, scaling, and clusteringprocesses were applied to the remaining cells. Integration ofgenome and epigenome data determined labels of clusters inUMAP of ATAC-seq data. T-cell and B-cell subpopulationswere selected to investigate differentially accessible chromatinregions and affected genes. Chr۱۸-۵۵۴۲۲۱۲۷-۵۵۴۲۴۱۹۶ isa transposon-accessible location related to the TCF۴ gene onchromosome ۱۸ that possibly affects the metastasis process.Conclusion: A differentially accessible region for the TCF۴gene was identified in B-cells and T-cells related to metastatic breast cancer

کلیدواژه ها:

Breast cancer ، B-cell ، T-cell ، scRNA-seq ، scATACseq ، differentially accessible chromatin region